These analyses examine the relationship between expression levels and viral titer for a set of genes that we hypothesize have a relationship with viral infection. The overall strategy is to:
Note: These analyses include only control and infected birds sacrificed at 1 day post-infection
aprioriAnalysis <- function(target, targetTissue, targetLevel, ...) {
result.tmp <- lcpm.all %>%
filter(levelGT == targetLevel,
identifier == target,
tissue == targetTissue) %>%
lm(lcpm ~ log.virus.sac, data = .) %>%
tidy(.) %>%
mutate(identifier = target) %>%
filter(term == "log.virus.sac") %>%
select(-term, -std.error, -statistic) %>%
pivot_longer(cols = estimate:p.value,
names_to = "result.type",
values_to = "results.value")
lcpm.all %>%
filter(levelGT == targetLevel,
identifier == target,
tissue == targetTissue) %>%
lm(lcpm ~ log.virus.sac, data = .) %>%
glance(.) %>%
mutate(identifier = target) %>%
select(r.squared, adj.r.squared, identifier) %>%
pivot_longer(cols = r.squared:adj.r.squared,
names_to = "result.type",
values_to = "results.value") %>%
rbind(result.tmp)
}
aprioriPlotting <- function(target, targetTissue, targetLevel, ...) {
ifelse(targetLevel == "gene",
statResults <- results.IG.tib %>%
filter(identifier == target),
statResults <- results.IT.tib %>%
filter(identifier == target))
annotation <- annot.all %>%
filter(transcript_id == target | gene_id == target) %>%
filter(sprot_geneName_BlastX != ".") %>%
select(sprot_geneName_BlastX) %>%
slice(1)
plot <- lcpm.all %>%
filter(levelGT == targetLevel,
identifier == target,
tissue == targetTissue) %>%
unite(birdLabel, bird, SSgroup.virus.sac, sep = "-") %>%
ggplot(aes(x = log.virus.sac, y = lcpm)) +
geom_point() +
geom_smooth(method = "lm") +
geom_text_repel(aes(label = birdLabel), ) +
ylab("Log2(Counts per million)") +
xlab("Log10(Viral titer + 1)") +
theme_classic() +
labs(title=paste0(annotation[1], " - ", target),
subtitle=paste0(targetTissue, " - ", targetLevel,
"; p = ", round(statResults[4,3], 5),
"; adj R2 = ", round(statResults[2,3], 3)))
print(plot)
}
| Tissue | Level | Analyzed | Significant |
|---|---|---|---|
| Bursa | Transcript | 1848 | 0 |
| Bursa | Gene | 762 | 0 |
| Ileum | Transcript | 1991 | 51 |
| Ileum | Gene | 812 | 42 |